SNP Report

Basic Info

Name	rs1538977 dbSNP Ensembl
Location	chr1:231761557 - 231761557(1)
Variant Alleles	A/G
Ancestral Allele	A
Minor Allele	G
Minor Allele Frequence	0.191094
Functional Annotation	intron_variant; NMD_transcript_variant.
Consequence to Transcript	intron_variant(ENST00000295051, ENST00000366632, ENST00000366633, ENST00000366636, ENST00000366637, ENST00000422590, ENST00000439617, ENST00000535944, ENST00000535983, ENST00000537876, ENST00000539444, ENST00000602281, ENST00000602567, ENST00000602634, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000602873, ENST00000602885, ENST00000602956, ENST00000602962, ENST00000620189, ENST00000622252, ENST00000628350); NMD_transcript_variant(ENST00000295051, ENST00000366632, ENST00000422590, ENST00000535944, ENST00000602567, ENST00000602634, ENST00000602700, ENST00000602713, ENST00000602822, ENST00000602885, ENST00000602956, ENST00000602962)
No. of Studies	4 (Positive: 0; Negative: 4; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 4)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Xiao, Y.,2011	A/G	A	Allelic permutated P-value = 0.999, genotypic permutated P-...... Allelic permutated P-value = 0.999, genotypic permutated P-value = 0.702 More...	No significant association was observed in BD. No significant association was observed in BD.	Negative
Palo, O. M., 2007	A/G		P-value = 0.718 in all patients, P-value = 0.058 in males, P...... P-value = 0.718 in all patients, P-value = 0.058 in males, P-value = 0.862 in females, with bipolar spectrum disorder More...		Negative
Yosifova, A.,2009	A/G		Allelic association: P-value = 0.27 Allelic association: P-value = 0.27	No significant association was observed No significant association was observed	Negative
Thomson, P. A.,2005(a)			Single-Marker Analysis: allele frequency, for BP, P-value = ...... Single-Marker Analysis: allele frequency, for BP, P-value = 0.49 More...	No significant association was observed. No significant association was observed.	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
TSNAX	translin-associated factor X	1q42.2	4(3/1/0)
DISC1	disrupted in schizophrenia 1	1q42.1	18(10/7/1)

SNPs in LD with rs1538977 (count: 5) View in gBrowse (chr1:231761169..231771101 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

rs_ID	Functional Annotation	r²[population]
rs1538976	intron_variant; NMD_transcript_variant	0.883[CEU]
rs3738402	3_prime_UTR_variant; intron_variant; NMD_transcript_variant; synonymous_variant	1.0[CHB]; 0.868[JPT]
rs16854940	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.802[CHD]; 0.868[JPT]
rs2793086	intron_variant; NMD_transcript_variant	0.883[CEU]; 0.874[TSI]
rs1538978	intron_variant; NMD_transcript_variant	0.827[CEU]

Overlap with SZ from cross-disorder studies (count: 1)

Reference	Statistical Result	Description	Result Category
Thomson, P. A.,2005(a)	Single-Marker Analysis:allele frequency, for SZ, P-value = 0.98	No significant association was observed.	Negative

Overlap with MDD from cross-disorder studies (count: 0)